When looking at my /etc/passwd, shadow, group, gshadow files I see some files is 0 size, others have a few users in...
every time my root user is missing... this requires me to boot into single mode, and use my backup files to restore those files.

Why does this happen ? I mean all my non ISPConfig (WebX_) users are missing and only a few of the WebX users are in the file ...

I checked and checked, re installed servers, moved from FC3 to FC6 etc etc ... version 2.2.6, 2.2.7, and 2.2.9 all does it.